"All decisions and cognition is unconscious"

I'm deeply troubled by the idea of an "unconscious". This is an idea created a century ago by Sigmund Freud; all modern psychotherapy schools seem to have inherited it, many psychologists (I mean experimental scientists) seem fine with the idea, and for the general public it's commonplace that we have "unconscious thoughts".

But how can you have an unconscious cognition? A cognition is an elementary moment of knowledge; how can such a thing be unconscious?

And how do people who treat consciousness as an emergent phenomenon deal with this "unconscious"? Is it an emergent phenomenon that is waiting to emerge? Seriously, I don't know, and I'd like to know.